Multiple sequence alignment - TraesCS4A01G192400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G192400 chr4A 100.000 2672 0 0 1 2672 472921679 472924350 0.000000e+00 4935.0
1 TraesCS4A01G192400 chr4A 94.960 377 17 2 2298 2672 692650625 692651001 8.240000e-165 590.0
2 TraesCS4A01G192400 chr4A 91.793 329 22 2 1973 2297 692650231 692650558 1.130000e-123 453.0
3 TraesCS4A01G192400 chr4A 82.639 144 18 5 1976 2117 733512559 733512421 1.300000e-23 121.0
4 TraesCS4A01G192400 chr4B 87.667 2019 147 50 1 1972 146494494 146492531 0.000000e+00 2255.0
5 TraesCS4A01G192400 chr4D 92.344 1463 70 16 471 1904 102164238 102162789 0.000000e+00 2043.0
6 TraesCS4A01G192400 chr5A 92.445 728 20 5 1976 2672 8137437 8136714 0.000000e+00 1007.0
7 TraesCS4A01G192400 chr3A 92.192 730 21 10 1974 2672 16458251 16458975 0.000000e+00 1000.0
8 TraesCS4A01G192400 chr5B 93.369 377 13 5 2298 2672 592808266 592808632 5.030000e-152 547.0
9 TraesCS4A01G192400 chr5B 91.159 328 23 2 1975 2298 592807875 592808200 8.780000e-120 440.0
10 TraesCS4A01G192400 chr1A 94.118 187 11 0 2368 2554 172408987 172409173 4.350000e-73 285.0
11 TraesCS4A01G192400 chr7D 77.755 481 62 18 1973 2412 163219267 163219743 1.230000e-63 254.0
12 TraesCS4A01G192400 chr7D 84.049 163 26 0 2508 2670 594000450 594000288 9.900000e-35 158.0
13 TraesCS4A01G192400 chr7D 91.667 48 4 0 2299 2346 1228024 1227977 1.720000e-07 67.6
14 TraesCS4A01G192400 chr7B 77.547 481 63 21 1973 2412 125209473 125209949 5.710000e-62 248.0
15 TraesCS4A01G192400 chr7B 76.458 480 64 25 1978 2412 125267562 125268037 5.790000e-52 215.0
16 TraesCS4A01G192400 chr7B 76.458 480 64 25 1978 2412 125303627 125304102 5.790000e-52 215.0
17 TraesCS4A01G192400 chr7B 76.250 480 65 25 1978 2412 125231386 125231861 2.700000e-50 209.0
18 TraesCS4A01G192400 chr7B 81.746 126 19 3 1964 2087 706230236 706230113 4.710000e-18 102.0
19 TraesCS4A01G192400 chr2B 93.333 90 5 1 1976 2064 105835820 105835909 6.000000e-27 132.0
20 TraesCS4A01G192400 chrUn 92.222 90 6 1 1976 2064 341595438 341595527 2.790000e-25 126.0
21 TraesCS4A01G192400 chr1B 84.348 115 14 3 1975 2087 434770541 434770429 2.810000e-20 110.0
22 TraesCS4A01G192400 chr3D 87.692 65 5 2 310 371 579034603 579034667 3.690000e-09 73.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G192400 chr4A 472921679 472924350 2671 False 4935.0 4935 100.0000 1 2672 1 chr4A.!!$F1 2671
1 TraesCS4A01G192400 chr4A 692650231 692651001 770 False 521.5 590 93.3765 1973 2672 2 chr4A.!!$F2 699
2 TraesCS4A01G192400 chr4B 146492531 146494494 1963 True 2255.0 2255 87.6670 1 1972 1 chr4B.!!$R1 1971
3 TraesCS4A01G192400 chr4D 102162789 102164238 1449 True 2043.0 2043 92.3440 471 1904 1 chr4D.!!$R1 1433
4 TraesCS4A01G192400 chr5A 8136714 8137437 723 True 1007.0 1007 92.4450 1976 2672 1 chr5A.!!$R1 696
5 TraesCS4A01G192400 chr3A 16458251 16458975 724 False 1000.0 1000 92.1920 1974 2672 1 chr3A.!!$F1 698
6 TraesCS4A01G192400 chr5B 592807875 592808632 757 False 493.5 547 92.2640 1975 2672 2 chr5B.!!$F1 697

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
295 296 0.026803 CAGTCCTTTTAGATGCGCGC 59.973 55.0 27.26 27.26 0.0 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1724 0.468214 TCTTCTCCGGCGAGATCCAT 60.468 55.0 9.3 0.0 44.68 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 5.320277 TCATGACCAAATGTATGTGGACAA 58.680 37.500 8.06 0.00 41.68 3.18
32 33 2.495669 CCAAATGTATGTGGACAACCCC 59.504 50.000 0.00 0.00 37.03 4.95
33 34 3.161067 CAAATGTATGTGGACAACCCCA 58.839 45.455 0.00 0.00 31.83 4.96
34 35 3.534357 AATGTATGTGGACAACCCCAA 57.466 42.857 0.00 0.00 38.06 4.12
41 42 3.850752 TGTGGACAACCCCAAACATATT 58.149 40.909 0.00 0.00 38.06 1.28
43 44 3.194755 GTGGACAACCCCAAACATATTCC 59.805 47.826 0.00 0.00 38.06 3.01
55 56 5.395546 CCAAACATATTCCTGGACATTTGGG 60.396 44.000 19.17 5.58 40.63 4.12
73 74 0.666374 GGGTCTTGTTTGGTGAACCG 59.334 55.000 0.00 0.00 39.43 4.44
77 78 3.460103 GTCTTGTTTGGTGAACCGTAGA 58.540 45.455 0.00 0.00 39.43 2.59
79 80 4.025145 GTCTTGTTTGGTGAACCGTAGAAG 60.025 45.833 0.00 0.47 39.43 2.85
92 93 3.195182 ACCGTAGAAGAAGTCTTAAGGGC 59.805 47.826 1.85 0.00 37.84 5.19
105 106 0.887387 TAAGGGCAACTCCAACGCAC 60.887 55.000 0.00 0.00 36.21 5.34
117 118 0.156446 CAACGCACGAACGCATTTTG 59.844 50.000 0.00 0.00 36.19 2.44
130 131 6.560253 AACGCATTTTGTCTGTTTAGATCT 57.440 33.333 0.00 0.00 34.94 2.75
132 133 5.470098 ACGCATTTTGTCTGTTTAGATCTGT 59.530 36.000 5.18 0.00 34.94 3.41
158 159 2.030007 ACAGAAATCACAACCCAATGCG 60.030 45.455 0.00 0.00 0.00 4.73
160 161 0.678395 AAATCACAACCCAATGCGCA 59.322 45.000 14.96 14.96 0.00 6.09
169 170 1.472480 ACCCAATGCGCAGACATAAAC 59.528 47.619 18.32 0.00 0.00 2.01
170 171 1.472082 CCCAATGCGCAGACATAAACA 59.528 47.619 18.32 0.00 0.00 2.83
171 172 2.518949 CCAATGCGCAGACATAAACAC 58.481 47.619 18.32 0.00 0.00 3.32
189 190 1.673400 CACGTTTTGTGTCCATGTGGA 59.327 47.619 0.00 0.00 43.88 4.02
213 214 0.034756 AAACCGCCTCAAATTTGGGC 59.965 50.000 27.56 27.56 39.56 5.36
214 215 0.831711 AACCGCCTCAAATTTGGGCT 60.832 50.000 30.90 19.73 40.27 5.19
228 229 2.649129 GGGCTGGGTTTGCATCCAC 61.649 63.158 10.02 0.00 0.00 4.02
236 237 1.599419 GGTTTGCATCCACACGAACAC 60.599 52.381 0.00 0.00 32.72 3.32
241 242 1.996292 CATCCACACGAACACGAGAT 58.004 50.000 0.00 0.00 0.00 2.75
242 243 2.734175 GCATCCACACGAACACGAGATA 60.734 50.000 0.00 0.00 0.00 1.98
243 244 2.913777 TCCACACGAACACGAGATAG 57.086 50.000 0.00 0.00 0.00 2.08
244 245 2.429478 TCCACACGAACACGAGATAGA 58.571 47.619 0.00 0.00 0.00 1.98
246 247 2.095415 CCACACGAACACGAGATAGACA 60.095 50.000 0.00 0.00 0.00 3.41
248 249 2.551032 ACACGAACACGAGATAGACACA 59.449 45.455 0.00 0.00 0.00 3.72
255 256 1.138883 GAGATAGACACACCGCGCA 59.861 57.895 8.75 0.00 0.00 6.09
291 292 3.206964 GCCCTACAGTCCTTTTAGATGC 58.793 50.000 0.00 0.00 0.00 3.91
294 295 1.359848 ACAGTCCTTTTAGATGCGCG 58.640 50.000 0.00 0.00 0.00 6.86
295 296 0.026803 CAGTCCTTTTAGATGCGCGC 59.973 55.000 27.26 27.26 0.00 6.86
297 298 2.351210 CCTTTTAGATGCGCGCGC 60.351 61.111 45.02 45.02 42.35 6.86
331 332 1.775385 CCCACTCTTCTCCCTCTCTC 58.225 60.000 0.00 0.00 0.00 3.20
341 342 2.674220 CCCTCTCTCTGCCCCCAAC 61.674 68.421 0.00 0.00 0.00 3.77
373 374 1.341581 GCCCAACCCTAGCCATTGTTA 60.342 52.381 0.00 0.00 0.00 2.41
375 376 2.014128 CCAACCCTAGCCATTGTTACG 58.986 52.381 0.00 0.00 0.00 3.18
381 382 2.748647 GCCATTGTTACGGCCGGT 60.749 61.111 31.76 17.55 42.82 5.28
399 400 1.532316 TCGGAGAGGGTTTCGGTGT 60.532 57.895 0.00 0.00 0.00 4.16
401 402 1.080025 GGAGAGGGTTTCGGTGTCG 60.080 63.158 0.00 0.00 37.82 4.35
408 409 1.375523 GTTTCGGTGTCGGCCATCT 60.376 57.895 2.24 0.00 36.95 2.90
410 411 1.822114 TTTCGGTGTCGGCCATCTCA 61.822 55.000 2.24 0.00 36.95 3.27
423 424 1.075970 ATCTCAGCCTCCAGCCGTA 60.076 57.895 0.00 0.00 45.47 4.02
424 425 0.470833 ATCTCAGCCTCCAGCCGTAT 60.471 55.000 0.00 0.00 45.47 3.06
425 426 1.068753 CTCAGCCTCCAGCCGTATG 59.931 63.158 0.00 0.00 45.47 2.39
426 427 2.590007 CAGCCTCCAGCCGTATGC 60.590 66.667 0.00 0.00 45.47 3.14
445 446 1.369448 GCGAGCTCGAGATACACCG 60.369 63.158 38.74 11.05 43.02 4.94
449 450 2.331805 CTCGAGATACACCGCCGG 59.668 66.667 6.58 0.00 0.00 6.13
450 451 3.825833 CTCGAGATACACCGCCGGC 62.826 68.421 19.07 19.07 0.00 6.13
451 452 4.201679 CGAGATACACCGCCGGCA 62.202 66.667 28.98 6.55 0.00 5.69
452 453 2.585247 GAGATACACCGCCGGCAC 60.585 66.667 28.98 7.95 0.00 5.01
453 454 3.075005 AGATACACCGCCGGCACT 61.075 61.111 28.98 7.23 0.00 4.40
464 465 4.154347 CGGCACTGAGCTCTCCCC 62.154 72.222 16.19 8.99 44.79 4.81
466 467 3.071206 GCACTGAGCTCTCCCCGA 61.071 66.667 16.19 0.00 41.15 5.14
471 472 1.671901 CTGAGCTCTCCCCGAAGACC 61.672 65.000 16.19 0.00 0.00 3.85
482 483 1.038130 CCGAAGACCTCCTCCACGAT 61.038 60.000 0.00 0.00 0.00 3.73
502 503 1.412710 TCCGGCATAGGATGTTGACTC 59.587 52.381 0.00 0.00 34.92 3.36
511 512 1.135199 GGATGTTGACTCGCCGAACTA 60.135 52.381 0.00 0.00 0.00 2.24
516 517 1.062206 GACTCGCCGAACTAGGACG 59.938 63.158 0.00 0.00 34.02 4.79
602 603 0.392461 GTCCACCAGCGGCTATTGAA 60.392 55.000 0.26 0.00 0.00 2.69
653 654 3.319198 AAGAAGGCCGGCGAGGAA 61.319 61.111 22.54 0.00 45.00 3.36
654 655 2.890766 AAGAAGGCCGGCGAGGAAA 61.891 57.895 22.54 0.00 45.00 3.13
744 773 1.257750 GGAGTTGGATTTGCCCCCAC 61.258 60.000 0.00 0.00 34.97 4.61
745 774 1.229177 AGTTGGATTTGCCCCCACC 60.229 57.895 0.00 0.00 34.97 4.61
746 775 2.121608 TTGGATTTGCCCCCACCC 59.878 61.111 0.00 0.00 34.97 4.61
747 776 3.554383 TTGGATTTGCCCCCACCCC 62.554 63.158 0.00 0.00 34.97 4.95
748 777 4.004635 GGATTTGCCCCCACCCCA 62.005 66.667 0.00 0.00 0.00 4.96
797 826 8.372877 TGATAATCAAAAGGCCCAAAGAAATA 57.627 30.769 0.00 0.00 0.00 1.40
827 858 6.786967 ATTAAGAAATCTCAAGCAGGCAAT 57.213 33.333 0.00 0.00 0.00 3.56
836 867 4.080695 TCTCAAGCAGGCAATCTATGAAGT 60.081 41.667 0.00 0.00 0.00 3.01
839 870 5.124457 TCAAGCAGGCAATCTATGAAGTTTC 59.876 40.000 0.00 0.00 0.00 2.78
840 871 3.950395 AGCAGGCAATCTATGAAGTTTCC 59.050 43.478 0.00 0.00 0.00 3.13
846 877 7.543520 CAGGCAATCTATGAAGTTTCCTTTTTC 59.456 37.037 0.00 0.00 0.00 2.29
862 893 4.261447 CCTTTTTCCGTTCCTGTTAACCAG 60.261 45.833 2.48 0.89 41.15 4.00
867 898 3.135167 TCCGTTCCTGTTAACCAGTTCTT 59.865 43.478 2.48 0.00 39.74 2.52
922 953 3.349006 CTGTGCGGTGCTGTCCAC 61.349 66.667 0.00 0.00 43.90 4.02
961 996 1.929230 TCGTCAACAGCTCGTCAAAA 58.071 45.000 0.00 0.00 0.00 2.44
998 1033 1.730902 CTACGCCATCGCATCCTCG 60.731 63.158 0.00 0.00 39.84 4.63
999 1034 3.207547 TACGCCATCGCATCCTCGG 62.208 63.158 0.00 0.00 39.84 4.63
1000 1035 4.284860 CGCCATCGCATCCTCGGA 62.285 66.667 0.00 0.00 34.03 4.55
1001 1036 2.345244 GCCATCGCATCCTCGGAT 59.655 61.111 0.00 0.00 34.81 4.18
1314 1355 1.074248 GTCCGTCCACAACCCCAAT 59.926 57.895 0.00 0.00 0.00 3.16
1511 1552 3.062466 CGAGGACGTGGAGAGCCA 61.062 66.667 0.00 0.00 43.47 4.75
1657 1698 4.030452 GCCACGAGTGCAACAGCC 62.030 66.667 0.00 0.00 41.43 4.85
1683 1724 0.466372 AGCTCTGACCCGATGATCGA 60.466 55.000 17.52 0.00 43.74 3.59
1684 1725 0.600557 GCTCTGACCCGATGATCGAT 59.399 55.000 17.52 0.00 43.74 3.59
1708 1766 2.897350 CGCCGGAGAAGATTGGGC 60.897 66.667 5.05 0.00 40.36 5.36
1803 1861 2.408032 GCGGTTACACGTTCGATACAAA 59.592 45.455 0.00 0.00 35.98 2.83
1853 1926 3.383026 GCAAAATCGATGCGTGTGT 57.617 47.368 0.00 0.00 33.57 3.72
1956 2029 4.644163 TTTTTAGGAAATCACCGAGGGA 57.356 40.909 0.00 0.00 34.73 4.20
1966 2039 1.075698 TCACCGAGGGAAGAGTTCTCT 59.924 52.381 0.00 0.00 45.03 3.10
2033 2106 2.758009 CCAACATTTTGGTCAAGCTGG 58.242 47.619 2.21 0.00 46.63 4.85
2142 2230 6.061022 TGGTAGAAGCAAGACAATATGGAA 57.939 37.500 0.00 0.00 0.00 3.53
2157 2245 8.765488 ACAATATGGAATTCAACATCACCATA 57.235 30.769 7.93 0.00 42.09 2.74
2208 2296 3.482110 GTGCATTCACGAGAACACAAAAC 59.518 43.478 10.16 0.00 36.39 2.43
2257 2349 0.737367 CGTGAATGCGAGAGAGGCAA 60.737 55.000 0.00 0.00 44.66 4.52
2414 2573 8.484641 TTTCTCTATAGACAATGCACTTGAAG 57.515 34.615 13.53 0.00 38.29 3.02
2463 2623 4.247380 CCTGATCCCTGCCGCCTC 62.247 72.222 0.00 0.00 0.00 4.70
2504 2665 2.270858 TGTTATTGTGGCCCTAGACCA 58.729 47.619 0.00 0.64 33.84 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 2.652348 TGTCCAGGAATATGTTTGGGGT 59.348 45.455 0.00 0.00 0.00 4.95
32 33 5.395546 CCCCAAATGTCCAGGAATATGTTTG 60.396 44.000 0.00 0.00 0.00 2.93
33 34 4.716287 CCCCAAATGTCCAGGAATATGTTT 59.284 41.667 0.00 0.00 0.00 2.83
34 35 4.264804 ACCCCAAATGTCCAGGAATATGTT 60.265 41.667 0.00 0.00 0.00 2.71
41 42 1.075374 CAAGACCCCAAATGTCCAGGA 59.925 52.381 0.00 0.00 33.09 3.86
43 44 2.292828 ACAAGACCCCAAATGTCCAG 57.707 50.000 0.00 0.00 33.09 3.86
55 56 1.385528 ACGGTTCACCAAACAAGACC 58.614 50.000 0.00 0.00 39.81 3.85
73 74 5.795972 AGTTGCCCTTAAGACTTCTTCTAC 58.204 41.667 3.36 0.00 37.40 2.59
77 78 3.394606 TGGAGTTGCCCTTAAGACTTCTT 59.605 43.478 3.36 0.00 36.49 2.52
79 80 3.418684 TGGAGTTGCCCTTAAGACTTC 57.581 47.619 3.36 0.00 34.97 3.01
92 93 1.083657 CGTTCGTGCGTTGGAGTTG 60.084 57.895 0.00 0.00 0.00 3.16
105 106 4.768145 TCTAAACAGACAAAATGCGTTCG 58.232 39.130 0.00 0.00 0.00 3.95
117 118 4.795268 TGTCGACACAGATCTAAACAGAC 58.205 43.478 15.76 4.03 0.00 3.51
130 131 2.869801 GGTTGTGATTTCTGTCGACACA 59.130 45.455 15.76 8.01 39.22 3.72
132 133 2.158885 TGGGTTGTGATTTCTGTCGACA 60.159 45.455 18.88 18.88 0.00 4.35
149 150 1.472480 GTTTATGTCTGCGCATTGGGT 59.528 47.619 12.24 0.00 0.00 4.51
158 159 4.929315 CACAAAACGTGTTTATGTCTGC 57.071 40.909 0.00 0.00 38.92 4.26
170 171 2.045561 TCCACATGGACACAAAACGT 57.954 45.000 0.00 0.00 39.78 3.99
189 190 0.387565 AATTTGAGGCGGTTTTGCGT 59.612 45.000 0.00 0.00 35.06 5.24
196 197 1.228862 AGCCCAAATTTGAGGCGGT 60.229 52.632 29.28 18.67 44.23 5.68
213 214 0.888736 TCGTGTGGATGCAAACCCAG 60.889 55.000 1.40 0.00 32.28 4.45
214 215 0.466372 TTCGTGTGGATGCAAACCCA 60.466 50.000 1.40 6.33 0.00 4.51
228 229 2.909244 GTGTGTCTATCTCGTGTTCGTG 59.091 50.000 0.00 0.00 38.33 4.35
236 237 1.939785 GCGCGGTGTGTCTATCTCG 60.940 63.158 8.83 0.00 0.00 4.04
241 242 1.803922 CGAATGCGCGGTGTGTCTA 60.804 57.895 8.83 0.00 0.00 2.59
242 243 3.112075 CGAATGCGCGGTGTGTCT 61.112 61.111 8.83 0.00 0.00 3.41
255 256 2.125512 GGCGGACACTGAGCGAAT 60.126 61.111 0.00 0.00 0.00 3.34
263 264 1.982938 GGACTGTAGGGCGGACACT 60.983 63.158 0.00 0.00 0.00 3.55
264 265 1.542187 AAGGACTGTAGGGCGGACAC 61.542 60.000 0.00 0.00 0.00 3.67
304 305 4.821589 GAAGAGTGGGCGCTCCGG 62.822 72.222 3.94 0.00 38.76 5.14
305 306 3.708220 GAGAAGAGTGGGCGCTCCG 62.708 68.421 3.94 0.00 38.76 4.63
306 307 2.185608 GAGAAGAGTGGGCGCTCC 59.814 66.667 3.94 6.36 36.20 4.70
307 308 2.185608 GGAGAAGAGTGGGCGCTC 59.814 66.667 7.64 2.47 35.82 5.03
308 309 3.394836 GGGAGAAGAGTGGGCGCT 61.395 66.667 7.64 0.00 0.00 5.92
309 310 3.378399 GAGGGAGAAGAGTGGGCGC 62.378 68.421 0.00 0.00 0.00 6.53
341 342 1.883084 GTTGGGCACTATCGAGCGG 60.883 63.158 0.00 0.00 0.00 5.52
377 378 2.577593 GAAACCCTCTCCGACCGG 59.422 66.667 0.00 0.00 0.00 5.28
378 379 2.181021 CGAAACCCTCTCCGACCG 59.819 66.667 0.00 0.00 0.00 4.79
381 382 1.530013 GACACCGAAACCCTCTCCGA 61.530 60.000 0.00 0.00 0.00 4.55
410 411 4.227134 CGCATACGGCTGGAGGCT 62.227 66.667 13.42 0.00 41.67 4.58
423 424 1.081774 GTATCTCGAGCTCGCGCAT 60.082 57.895 30.97 21.96 39.10 4.73
424 425 2.328289 GTATCTCGAGCTCGCGCA 59.672 61.111 30.97 16.77 39.10 6.09
425 426 2.006587 GTGTATCTCGAGCTCGCGC 61.007 63.158 30.97 18.59 39.60 6.86
426 427 1.369448 GGTGTATCTCGAGCTCGCG 60.369 63.158 30.97 25.39 39.60 5.87
427 428 1.369448 CGGTGTATCTCGAGCTCGC 60.369 63.158 30.97 16.87 39.60 5.03
435 436 2.585247 GTGCCGGCGGTGTATCTC 60.585 66.667 28.82 9.29 0.00 2.75
445 446 4.828925 GGAGAGCTCAGTGCCGGC 62.829 72.222 22.73 22.73 44.23 6.13
449 450 2.570582 CTTCGGGGAGAGCTCAGTGC 62.571 65.000 17.77 0.53 43.29 4.40
450 451 0.967887 TCTTCGGGGAGAGCTCAGTG 60.968 60.000 17.77 0.69 0.00 3.66
451 452 0.968393 GTCTTCGGGGAGAGCTCAGT 60.968 60.000 17.77 0.00 0.00 3.41
452 453 1.671901 GGTCTTCGGGGAGAGCTCAG 61.672 65.000 17.77 2.28 40.20 3.35
453 454 1.682684 GGTCTTCGGGGAGAGCTCA 60.683 63.158 17.77 0.00 40.20 4.26
464 465 0.382515 GATCGTGGAGGAGGTCTTCG 59.617 60.000 0.00 0.00 0.00 3.79
466 467 1.038130 CGGATCGTGGAGGAGGTCTT 61.038 60.000 0.00 0.00 0.00 3.01
471 472 1.179174 TATGCCGGATCGTGGAGGAG 61.179 60.000 5.05 0.00 0.00 3.69
482 483 1.412710 GAGTCAACATCCTATGCCGGA 59.587 52.381 5.05 0.00 37.50 5.14
494 495 0.242825 CCTAGTTCGGCGAGTCAACA 59.757 55.000 10.46 0.00 0.00 3.33
497 498 1.642037 CGTCCTAGTTCGGCGAGTCA 61.642 60.000 10.46 0.00 0.00 3.41
511 512 2.113139 CCACAAACCAGGCGTCCT 59.887 61.111 0.00 0.00 0.00 3.85
516 517 2.617274 GCTCGTCCACAAACCAGGC 61.617 63.158 0.00 0.00 0.00 4.85
524 525 2.432456 GCATCGTGCTCGTCCACA 60.432 61.111 8.17 0.00 40.96 4.17
547 548 2.603776 AGGCGAAGAAGGACCGGT 60.604 61.111 6.92 6.92 0.00 5.28
581 582 1.091771 CAATAGCCGCTGGTGGACTG 61.092 60.000 2.16 0.00 0.00 3.51
596 597 3.107601 CTCACCTGTCTCCCCTTCAATA 58.892 50.000 0.00 0.00 0.00 1.90
602 603 2.284995 GCCTCACCTGTCTCCCCT 60.285 66.667 0.00 0.00 0.00 4.79
680 684 2.279743 GGATCAATGCCAGGCCCA 59.720 61.111 9.64 0.00 0.00 5.36
744 773 7.417116 CCAGACATTTTCATTCTTATCTTGGGG 60.417 40.741 0.00 0.00 0.00 4.96
745 774 7.340232 TCCAGACATTTTCATTCTTATCTTGGG 59.660 37.037 0.00 0.00 0.00 4.12
746 775 8.284945 TCCAGACATTTTCATTCTTATCTTGG 57.715 34.615 0.00 0.00 0.00 3.61
747 776 9.731819 CATCCAGACATTTTCATTCTTATCTTG 57.268 33.333 0.00 0.00 0.00 3.02
748 777 9.690913 TCATCCAGACATTTTCATTCTTATCTT 57.309 29.630 0.00 0.00 0.00 2.40
814 845 4.197750 ACTTCATAGATTGCCTGCTTGAG 58.802 43.478 0.00 0.00 0.00 3.02
836 867 5.163530 GGTTAACAGGAACGGAAAAAGGAAA 60.164 40.000 8.10 0.00 0.00 3.13
839 870 3.633065 TGGTTAACAGGAACGGAAAAAGG 59.367 43.478 8.10 0.00 0.00 3.11
840 871 4.855531 CTGGTTAACAGGAACGGAAAAAG 58.144 43.478 8.10 0.00 43.70 2.27
862 893 1.268640 TGGTTACCGCGCAAAAAGAAC 60.269 47.619 8.75 2.11 0.00 3.01
867 898 1.337071 TGAATTGGTTACCGCGCAAAA 59.663 42.857 8.75 0.00 0.00 2.44
961 996 3.420482 CAAGGCCGGGGAGGGAAT 61.420 66.667 2.18 0.00 41.48 3.01
998 1033 2.123295 GGGACCCCATTGCCATCC 60.123 66.667 0.00 0.00 35.81 3.51
1268 1309 1.534235 AGGAGCGTGAGGTTGAGGT 60.534 57.895 0.00 0.00 45.11 3.85
1314 1355 1.684734 GTAGGTGAAGGAGGCCGGA 60.685 63.158 5.05 0.00 0.00 5.14
1341 1382 1.813753 CGATAGGTTGGTGTGGCCG 60.814 63.158 0.00 0.00 41.21 6.13
1683 1724 0.468214 TCTTCTCCGGCGAGATCCAT 60.468 55.000 9.30 0.00 44.68 3.41
1684 1725 0.468214 ATCTTCTCCGGCGAGATCCA 60.468 55.000 9.30 0.00 44.68 3.41
1803 1861 6.332630 CGCTGTTTAAATTTCAATCCTCCAT 58.667 36.000 0.00 0.00 0.00 3.41
1853 1926 1.530720 TCTCGCACGTACGTGTAGAAA 59.469 47.619 39.56 26.82 46.90 2.52
1956 2029 8.967664 ATCTAGTATAACGTGAGAGAACTCTT 57.032 34.615 5.80 0.00 42.99 2.85
1966 2039 5.390251 GCGATTCCGATCTAGTATAACGTGA 60.390 44.000 0.00 0.00 38.22 4.35
1969 2042 4.020518 CGCGATTCCGATCTAGTATAACG 58.979 47.826 0.00 0.00 38.22 3.18
2031 2104 9.038072 TGGATTACTACTGACTTAACATTACCA 57.962 33.333 0.00 0.00 0.00 3.25
2142 2230 8.450578 ACGATAATGTTATGGTGATGTTGAAT 57.549 30.769 0.00 0.00 32.03 2.57
2157 2245 3.494626 CGATGCTGCCTTACGATAATGTT 59.505 43.478 0.00 0.00 0.00 2.71
2208 2296 9.639601 TTAGTATCAGACTTAATGTCAAGTGTG 57.360 33.333 6.77 6.77 46.08 3.82
2257 2349 9.664332 GTTTTATCATGCTCATACTCTATCCAT 57.336 33.333 0.00 0.00 0.00 3.41
2414 2573 3.643159 ATGTTCCTTTGCCTTCGAAAC 57.357 42.857 0.00 0.00 0.00 2.78
2463 2623 3.354089 ACAATTGGTCAAGCTTTGTCG 57.646 42.857 10.83 0.00 0.00 4.35


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.